Our long range goal is the elucidation of the molecular mechanisms responsible for the differential expression of genes in specialized mammalian cells, as a basis for better understanding and treatment of human health problems caused by defects in cell differentiation, including aging and cancer. The tissue-specific pattern of gene expression is reflected in a corresponding pattern of different chromatin conformation. The primary determinants of chromatin conformation are the histones. We have described a number of nonallelic primary structure variants of mammalian histones which are expressed under different circumstances and occur in different proportions in adult tissues. In order to elucidate the specific functions of each histone species and its variants, we are defining on the molecular level the properties and dynamics of specific protein-protein and protein-DNA interactions which are responsible for different aspects of nucleosome architecture and chromatin conformation. For this purpose we have developed protein "footprinting" assays which measure simultaneously the degree of protection of a large number of specific sites in the presumptive binding domains of the core histones. These assays will be used to compare nucleosomes containing different variants as well as chromatin in different functional states.